scatterPlot: scatterPlot Plot GO terms as scattered points.

In rrvgo: Reduce + Visualize GO

Description

scatterPlot Plot GO terms as scattered points.

Usage

scatterPlot(
  simMatrix,
  reducedTerms,
  size = "score",
  addLabel = TRUE,
  labelSize = 3
)

Arguments

simMatrix	a (square) similarity matrix.
reducedTerms	a data.frame with the reduced terms from reduceSimMatrix()
size	what to use as point size. Can be either GO term's "size" or "score"
addLabel	add labels with the most representative term of the group.
labelSize	text size in the label.

Details

Distances between points represent the similarity between terms. Axes are the first 2 components of applying a PCoA to the (di)similarity matrix. Size of the point represents the provided scores or, in its absence, the number of genes the GO term contains.

Value

ggplot2 object raedy to be printed (or manipulated)

Examples

go_analysis <- read.delim(system.file("extdata/example.txt", package="rrvgo"))
simMatrix <- calculateSimMatrix(go_analysis$ID, orgdb="org.Hs.eg.db", ont="BP", method="Rel")
scores <- setNames(-log10(go_analysis$qvalue), go_analysis$ID)
reducedTerms <- reduceSimMatrix(simMatrix, scores, threshold=0.7, orgdb="org.Hs.eg.db")
scatterPlot(simMatrix, reducedTerms)

rrvgo documentation built on Nov. 8, 2020, 6:17 p.m.